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Previous studies on the taxonomy of Babesia spp. (phylum Apicomplexa) using morphological and life cycle characteristics have resulted in their classification into 3 subgenera, with the genus Theileria being most closely related to them. Using a strategy based on the direct sequence analysis of products derived by asymmetric PCR to determine the nucleotide sequences, we have tested the validity of this classification by sequencing the small subunit ribosomal RNA genes amplified from 2 Babesia species, namely Babesia bovis and Babesia rodhaini, and comparing these with previously published sequences of Theileria annulata and Babesia bigemina using Plasmodium falciparum as an outgroup. The results of this phylogenetic analysis support the recognition of at least 2 genera in Babesia--one to include B. bigemina and B. bovis, the other to include B. rodhaini.

Three sets of rRNA genes (units 1S-3S) have been identified in Babesia bovis (Samford isolate). All three units are present in the same, probably single, copy number. The rRNA genes and flanking regions have been analysed by cloning, restriction mapping and DNA hybridization. The units are approximately 7 kb in length and have essentially identical restriction maps. In contrast the flanking regions exhibit significant restriction site differences. However, the regions upstream of all three units are related and sequences similar to part of the region upstream of units 1S and 3S are present in multiple copies in the genome. The downstream regions appear to be unrelated, but downstream from unit 1S is a region of at least 7 kb similar to a second region not closely linked to the rDNA units. The restriction enzyme site polymorphisms in the flanking regions of the equivalent units in different isolates allow ready discrimination among six different isolates of B. bovis.